Sympatric speciation, the formation of species in the absence of geographical barriers, remains one of the most contentious topics in evolutionary biology. Although sympatric speciation seems theoretically possible, only a few credible examples exist. Here, we report a possible case of sympatric speciation in medaka, the genus Oryzias, in Sulawesi. Interestingly, almost all Oryzias species are allopatrically distributed within the island. As exceptions, Oryzias nigrimas, O. orthognathus, and O. nebulosus are sympatrically distributed in Lake Poso, an ancient tectonic lake. They are closely related but different in ecology. To investigate whether they have reproductively isolated gene pools or not, we conducted morphological comparisons and population genetic analyses using mitochondrial haplotypes and genome-wide sequencing data. We found that these three species have differences in their morphology, especially in body shape and meristic characters. A phylogenetic network of mitochondrial DNA haplotypes was divided into two distinct groups: one composed of O. nigrimas and the other of O. orthognathus and O. nebulosus. Incomplete lineage sorting or introgression can explain this pattern. We discuss the results of population structure analyses using ddRAD-seq data and the possibility that they have diverged sympatrically.